@inproceedings{f2d2d454787d49d386dbcc177125b7c1,
title = "Parameter inference in differential equation models of biopathways using time warped gradient matching",
abstract = "Parameter inference in mechanistic models of biopathways based on systems of coupled differential equations is a topical yet computationally challenging problem due to the fact that each parameter adaptation involves a numerical integration of the differential equations. Techniques based on gradient matching, which aim to minimize the discrepancy between the slope of a data interpolant and the derivatives predicted from the differential equations, offer a computationally appealing shortcut to the inference problem. Gradient matching critically hinges on the smoothing scheme for function interpolation, with spurious oscillations in the interpolant having a dramatic effect on the subsequent inference. The present article demonstrates that a time warping approach that aims to homogenize intrinsic functional length scales can lead to a significant improvement in parameter estimation accuracy. We demonstrate the effectiveness of this scheme on noisy data from a dynamical system with periodic limit cycle, and a biopathway model.",
keywords = "Biopathways, Differential equations, Gradient matching, Optimisation, Reproducing kernel hilbert space, Time warping",
author = "Mu Niu and Simon Rogers and Maurizio Filippone and Dirk Husmeier",
note = "Publisher Copyright: {\textcopyright} Springer International Publishing AG 2017.; 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016 ; Conference date: 01-09-2016 Through 03-09-2016",
year = "2017",
doi = "10.1007/978-3-319-67834-4_12",
language = "English (US)",
isbn = "9783319678337",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "145--159",
editor = "Giulio Caravagna and Roberto Tagliaferri and David Gilbert and Andrea Bracciali",
booktitle = "Computational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Revised Selected Papers",
address = "Germany",
}